Pheweb data download - summary statistics

[Shicheng Guo]

Dear UMich pheweb team: 

I want to know how to download the summary statistic data for these different pheWeb server? 

Thanks. 

Datasets:

UKBiobank TOPMed-imputed: 1400 EHR-derived broad PheWAS codes for 57 million TOPMed-imputed variants in 400,000 white British individuals.

UKBiobank HRC-imputed: 1400 EHR-derived broad PheWAS codes for 20 million imputed variants in 400,000 white British individuals.

UKBiobank Neale v1: 2400 traits for 11 million imputed variants in 337,000 unrelated white British individuals.

MGI freeze2: 1700 EHR-derived broad PheWAS codes for 24 million imputed variants in 40,000 individuals.

MGI freeze1: 1400 EHR-derived broad PheWAS codes for 8 million imputed variants in 18,000 individuals.

MGI BioVU Labs Meta: 70 meta-analyzed phenotypes for 800,000 variants.

FinMetSeq: 60 phenotypes for 400,000 variants in 8000-19,000 individuals.

[Sarah Gagliano Taliun]

Hi! Thanks for your interest in PheWeb.

Below are the locations to download summary statistics for the instances of PheWeb you have listed:

UKBiobank TOPMed-imputed, FinMetSeq, MGI BioVU Labs Meta, MGI freeze1: on each phenotype page, there is a "Download summary statistics button" on the top right (above the Manhattan plot). This option is for a per-phenotype basis.

MGI freeze2: I am uncertain if the summary statistics are available for download. Sorry.

You can download all the summary statistics for the following instance of PheWeb. (Some of the other instances of PheWeb may also have similar types of repositories to download all summary statistics.)

UKBiobank HRC-imputed: https://www.leelabsg.org/resources (from the Lee lab)

UKBiobank Neale v1: http://www.nealelab.is/uk-biobank (the round1 results, but note that the Neale lab has since updated to round2, which are *not* displayed in this instance of PheWeb)

Sarah